Graduate Theses & Dissertations

Pages

Robust assessment of changes in wild mammal occupancy and activity relative to livestock and human disturbance
Anthropogenic activities such as human activity and livestock grazing are responsible for the global rise in disturbance impacts on wildlife and may underlie regional changes in biodiversity and ecosystem dynamics. Few studies have tried to disentangle the effects of different anthropogenic activities on wildlife behaviour, leaving a major gap in our understanding of conservation and management needs in disturbed areas. Human activity and livestock grazing are increasing in spread and intensity worldwide, thereby imposing pressure on both wildlife and natural areas. In this thesis, I used a camera trapping and occupancy modeling framework to assess whether human presence and livestock grazing had different impacts on site occupancy and activity of 10 wild mammal species, and how responses differed across taxa. Specifically, I predicted that all species would be sensitive to disturbance, but the type and intensity of the response would depend on disturbance type. I detected different responses to each disturbance type across species, but response type (displacement, activity change, crepuscularity) was not associated with species characteristics such as body. Importantly, disturbance intensity had a strong effect on wildlife activity levels, with many species exhibiting marked reductions in activity at high human or livestock disturbance intensity. It remains unclear whether all species’ responses are a direct consequence of disturbance versus indirect outcomes of shifts in behaviour of other species in the wildlife community (i.e., disturbance-related changes in prey activity may affect predator activity). Although on the whole disturbance intensity and effect sizes tended to be relatively low in this study, responses were exhibited across all species, implying that disturbance responses may be universal in wild mammals and largely underestimated. Ultimately, my work offers a template for the robust assessment of disturbance impacts on wildlife and provides new avenues for future research to deepen our understanding of wildlife sensitivity to anthropogenic activities. Author Keywords: activity, anthropogenic disturbance, human activity, livestock, occupancy, wildlife
SARS-CoV-2 Protein-based Detection Using Localized Surface Plasmon Resonance
During the COVID-19 pandemic, nucleic acid and antibody-based testing methods were heavily relied upon, but can be costly, time-consuming and exhibit high false -negative and -positive rates. Thus, alternative strategies are needed. Viral antigens such as the SARS-CoV-2 spike (S) glycoprotein are critical in the function of the virus and useful as diagnostic biomarkers for viral infections. For biosensing applications, aptamers are suitable high-affinity and cost-effective binding partners for their specific targets. Using localized surface plasmon resonance (LSPR), real-time, rapid acquisition of results can be achieved, essential for improving the efficacy of a sensor. Herein, LSPR aptamer sensors were fabricated for the detection of the SARS-CoV-2 protein. Data indicate that the best performing aptasensor was the streptavidin-biotin sensor, while the current gold aptasensor exhibited lower sensitivity and the fabrication of the carboxyl aptasensor was unsuccessful. The S1 aptamer selectively bound the S1 protein with high binding affinity. Excellent shelf-life stability, reusability, and high recovery in complex matrices was also maintained. Additionally, a receptor binding domain (RBD) functionalized sensor was fabricated to examine the interactions with angiotensin converting enzyme 2 (ACE2), for future assessment of inhibitors used in drug therapies. Overall, LSPR has been demonstrated as a viable tool for measuring SARS-CoV-2 related aptamer-protein and protein-protein interactions, and this strategy may be applied to other viral or non-viral antigen targets. Author Keywords: Antigen-based Detection, Coronavirus, COVID-19, Inhibition, Localized Surface Plasmon Resonance, SARS-CoV-2
SPATIAL AND TEMPORAL GENETIC STRUCTURE OF WOLVERINE POPULATIONS
Habitat loss and fragmentation can disrupt population connectivity, resulting in small, isolated populations and low genetic variability. Understanding connectivity patterns in space and time is critical in conservation and management planning, especially for wide-ranging species in northern latitudes where habitats are becoming increasingly fragmented. Wolverines (Gulo gulo) share similar life history traits observed in large-sized carnivores, and their low resiliency to disturbances limits wolverine persistence in modified or fragmented landscapes - making them a good indicator species for habitat connectivity. In this thesis, I used neutral microsatellite and mitochondrial DNA markers to investigate genetic connectivity patterns of wolverines for different temporal and spatial scales. Population genetic analyses of individuals from North America suggested wolverines west of James Bay in Canada are structured into two contemporary genetic clusters: an extant cluster at the eastern periphery of Manitoba and Ontario, and a northwestern core cluster. Haplotypic composition, however, suggested longstanding differences between the extant eastern periphery and northwestern core clusters. Phylogeographic analyses across the wolverine's Holarctic distribution supported a postglacial expansion from a glacial refugium near Beringia. Although Approximate Bayesian computations suggested a west-to-east stepping-stone divergence pattern across North America, a mismatch distribution indicated a historic bottleneck event approximately 400 generations ago likely influenced present-day patterns of haplotype distribution. I also used an individual-based genetic distance measure to identify landscape features potentially influencing pairwise genetic distances of wolverines in Manitoba and Ontario. Road density and mean spring snow cover were positively associated with genetic distances. Road density was associated with female genetic distance, while spring snow cover variance was associated with male genetic distance. My findings suggest that northward expanding anthropogenic disturbances have the potential to affect genetic connectivity. Overall, my findings suggest that (1) peripheral populations can harbour genetic variants not observed in core populations - increasing species genetic diversity; (2) historic bottlenecks can alter the genetic signature of glacial refugia, resulting in a disjunct distribution of unique genetic variants among contemporary populations; (3) increased temporal resolution of the individual-based genetic distance measure can help identify landscape features associated with genetic connectivity within a population, which may disrupt landscape connectivity. Author Keywords: conservation genetics, Holarctic species, landscape genetics, peripheral population, phylogeography, wolverine
Scarring, sex assignment, and sex-specific sociality of Indo-Pacific humpback dolphins (Sousa chinensis) in the Pearl River Estuary and eastern Taiwan Strait
The Pearl River Estuary (PRE) and eastern Taiwan Strait (ETS) populations of Indo-Pacific humpback dolphins (Sousa chinensis) contain ~600 and 100 catalogued individuals, respectively. Population demography is important for conservation actions but few animals have been sexed by conventional methods. Longitudinal analysis of tooth-rake scars on dorsal fins showed scars disappear within 7 months; sexing adults by scarring is likely not impacted by juvenile scarring. Using dorsal fin photographs, sex assigned for 87% of catalogued PRE adults (n=300) and for 93% of ETS adults (n=60), using scars hypothesized from male-male competition, was in concordance with sex assigned by DNA, calf association, and ventral photographs. Scarring was higher in presumed males than females and in PRE females than ETS females. Female:male sex ratios were 3:2 (PRE) and 2:1 (ETS), though this likely results from biases in photo-identification methods. Social analysis with presumed sexes showed strong female-female associations in both populations but stronger female-male and male-male associations in PRE. These results support sex differentiation by scarring, which was a non-invasive approach, and sex assignment for many PRE and ETS individuals. Author Keywords: Indo-Pacific humpback dolphins, photo-identification, scarring, sex differentiation, sexes, social structure
Seasonal habitat use and movement of native brook trout (Salvelinus fontinalis) in urban headwater streams
Coldwater streams are becoming increasingly impacted due to urbanization. Using environmental surveys, mark-recapture and telemetry, I assessed factors influencing seasonal brook trout (Salvelinus fontinalis) habitat use and movement in urban headwater streams in central Ontario between 2017-18. Generalized additive models were used to assess which habitat variables best explained seasonal yearling and older brook trout abundance, while generalized least squares models were used to assess overall trends in radio-tagged brook trout movement. My research demonstrated dynamic patterns in habitat use and movement by urban stream-dwelling brook trout. Yearlings were primarily influenced by water quality (stream temperature, conductivity), while older brook trout were most strongly influenced by stream morphology (depth, undercut bank). Movement occurred disproportionately around the spawning season and was more limited in the smaller, more altered stream. These findings may be used to inform fisheries managers on crucial timing and location of brook trout habitat refugia within urbanized environments. Author Keywords: Brook trout, coldwater stream, groundwater, habitat use, radiotelemetry, urbanization
Seasonal variation in nutrient and particulate inputs and outputs at an urban stormwater pond in Peterborough, Ontario
Stormwater ponds (SWPs) are a common feature in new urban developments where they are designed to minimize runoff peaks from impervious surfaces and retain particulate matter. As a consequence, SWPs can be efficient at retaining particle-bound nutrients, but may be less efficient at retaining nutrients that are present primarily in the dissolved form, like nitrogen (N). However, the forms of nutrients (e.g. particulate vs. dissolved) likely differ with hydrologic and seasonal conditions and few studies have examined year-round differences in nutrient forms and concentrations at urban SWPs. In order to contrast total suspended solids (TSS), phosphorus (P) and nitrogen (N) levels between low and high flow conditions, sampling was conducted at an urban SWP in Peterborough, ON between November 2012 and October 2013. Only an increase in TSS levels at the outflow between low and high flow conditions was observed, as well as a decrease in TSS levels at the outflow compared to Inflow 1 under low flow conditions. Nitrate-N (NO3-N) was the dominant form of N entering the pond under all flow conditions, whereas the fraction of total-P (TP) that was particulate increased under high flow conditions. Nevertheless, the dissolved fraction of TP was consistently high in these urban inlets. Only NO3-N was significantly greater in the inflows than outflow and only under low flow conditions. Increases in the proportions of organic-N and ammonium-N in the outlet suggest that biological processing is important for N retention. Author Keywords: nitrogen, Ontario, phosphorus, stormwater ponds, total suspended solids
Selection on functional genes across a flying squirrel (genus Glaucomys) hybrid zone
While hybridization between distinct taxa can have undesirable implications, it can also result in increased genetic variability and potentially, the exchange of adaptive genes or traits. Adaptive variation acquired through introgressive hybridization may be particularly advantageous for species facing rapid environmental change. I investigated a novel, climate change-induced hybrid zone between two flying squirrel species: the southern (Glaucomys volans) and northern (G. sabrinus) flying squirrel. I was interested in the occurrence of hybridization and introgression, the type of selective pressures maintaining the hybrid zone and the potential for adaptive introgression. I found relatively low hybridization and introgression frequencies (1.7% and 2.9% of the population, respectively) and no evidence of selection on hybrids or backcrosses in particular environments. I conclude that the data are more consistent with a hybrid zone maintained by endogenous (environment-independent) selection. I tested for adaptive introgression using two functional genes: IGF-1 and CLOCK. I documented intermediate functional allele frequencies in backcrosses compared to parental populations, suggesting the alleles do not confer fitness advantages in backcrosses. Despite lack of evidence for current adaptive introgression, genetic admixture between G. volans and G. sabrinus may provide adaptive potential should these species face more rapid or drastic environmental change in the future. Author Keywords: adaptive introgression, flying squirrel, Glaucomys sabrinus, Glaucomys volans, hybridization, introgression
Sensitivity of Forest Soils to Acidic Deposition Downwind of an Aluminum Smelter, Kitimat, B.C.
Maximum permitted SO2 emissions from an aluminum smelter in Kitimat, B.C., increased after modernization in 2015. An increase in acidic deposition can potentially acidify forest soils. Monitoring was conducted at two long-term soil monitoring plots at near (7 km) and far (41 km) sites downwind from the smelter. Change in soil properties was assessed between 2015 and 2018: for the near plot, there was significant decrease in pH and exchange acidity; far plot soils exhibited significant decrease of base cations and exchange acidity in the 0–5 cm layer only. The average total SO42- deposition at near and far plots were estimated to be between 8.2–12.1 and 6.7–7.4 kg/ha/yr, respectively. It was concluded no soil acidification was detected. Observed changes were attributed to measured differences in organic matter, likely influenced by sampling difficulty and measurement process discrepancies. Estimated SO42- deposition levels pose no risk to soil base cation depletion. Author Keywords: acid forest soils, acidic deposition, aluminum smelter, exchangeable base cations, long-term monitoring, minimum detectable change
Sex-Specific Graphs
Sex-specific genetic structure is a commonly observed pattern among vertebrate species. Facing differential selective pressures, individuals may adopt sex-specific life historical traits that ultimately shape genetic variation among populations. Although differential dispersal dynamics are commonly detected in the literature, few studies have investigated the potential effect of sex-specific functional connectivity on genetic structure. The recent uses of Graph Theory in landscape genetics have demonstrated network capacities to describe complex system behaviors where network topology intuitively represents genetic interaction among sub-units. By implementing a sex-specific network approach, our results suggest that Sex-Specific Graphs (SSG) are sensitive to differential male and female dispersal dynamics of a fisher (Martes pennanti) metapopulation in southern Ontario. Our analyses based on SSG topologies supported the hypothesis of male-biased dispersal. Furthermore, we demonstrated that the effect of the landscape, identified at the population-level, could be partitioned among sex-specific strata. We found that female connectivity was negatively affected by snow depth, while being neutral for males. Our findings underlined the potential of conducting sex-specific analysis by identifying landscape elements that promotes or impedes functional connectivity of wildlife populations, which sometimes remains cryptic when studied at the population level. We propose that SSG approach would be applicable to other vagile species where differential sex-specific processes are expected to occur. Author Keywords: genetic structure, Landscape Genetics, Martes pennanti, Population Graph, sex-biased dispersal, Sex-Specific Graphs
Sexual Dimporphism and Population Dynamics of Sub-Arctic Breding Dunlin (Calidris alpina hudsonia) near Churchill, Manitoba, Canada
Around the world, many populations of migratory shorebirds appear to be declining. Conservation strategies to reverse declining trends rely on, among other information, a firm understanding of breeding ground population dynamics. From 2010 to 2014, I studied a breeding population of Dunlin (Calidris alpina hudsonia) near Churchill, Manitoba using mark-recapture methods. I found that females were significantly larger than males. I subsequently developed an equation based on morphological features that successfully classified 87.1% of females and 92.6% of males, sexed using molecular techniques. Using program MARK, I quantified the annual apparent survival of adults (± SE) within the breeding population (0.82 ± 0.063 for males, 0.73 ± 0.12 for females). Transient adults made up a significant percentage of the female population (32%, P = 0.011), but non-significant in the male population (12%, P > 0.05). Re-sight rate was high for both sexes, and ranged from 0.86-0.90 per year. Sex, year, and nest initiation date were the factors that had the greatest influence on annual returns. There was no significant difference in mean inter-annual nest site distance between sexes (male: 82.01 ± 13.42 m, female: 208.38 ± 55.88 m, P > 0.05). The high survival estimates obtained in this study suggest that the breeding population is stable and may not be contributing to suspected population declines within the subspecies. Author Keywords: demography, discriminant function analysis, mark-recapture, sexual size dimorphism, survival
Shorebird Habitat Use and Foraging Ecology on Bulls Island, South Carolina During the Non-Breeding Season
Recent declines in North American shorebird populations could be linked to habitat loss on the non-breeding grounds. Sea-level rise and increased frequency of coastal storms are causing significant erosion of barrier islands, thereby threatening shorebirds who rely on shoreline habitats for foraging. I conducted shorebird surveys on Bulls Island, South Carolina in the winters of 2018 and 2019 and examined habitat selection and foraging behaviour in Dunlin (Calidris alpina), Sanderling (Calidris alba), Semipalmated Plovers (Charadrius semipalmatus), and Piping Plovers (Charadrius melodus). Area, tidal stage, and invertebrate prey availability were important determinants of shorebird abundance, behaviour, and distribution. My study highlights the importance of Bulls Island’s habitat heterogeneity to supporting a diverse community of non-breeding shorebirds. Considering both the high rate of erosion and the increased frequency of disturbance along the shoreline of the island, intertidal habitats should be monitored to predict negative effects of changes in habitat composition and area on non-breeding shorebirds. Author Keywords: foraging behaviour, habitat loss, habitat selection, invertebrate prey, non-breeding, shorebirds
Shorebird Stopover Ecology and Environmental Change at James Bay, Ontario, Canada
I examined how shorebirds respond to environmental change at a key subarctic migratory bird stopover site, the southwestern coast of James Bay, Ontario, Canada. First, I investigated if the morphology of sandpipers using James Bay during southbound migration has changed compared to 40 years prior. I found shorter, more convex and maneuverable wings for sandpipers in the present-day compared to the historical monitoring period, which supports the hypothesis that wing length change is driven by increases in predation risk. Secondly, I assessed the relationship between migration distance, body condition, and shorebird stopover and migratory decisions. Species that travelled farther distances from James Bay to wintering areas migrated with more characteristics of a time-minimizing migration strategy whereas species that travelled shorter distances migrated with energy minimizing strategies. Body condition impacted length of stay, wind selectivity at departure, groundspeeds, and probability of stopover and detection in North America after departing James Bay. Thirdly, I examined annual variation in dry/wet conditions at James Bay and found that shorebirds had lower body mass in years with moderate drought. In the present-day, drought resulted in lower invertebrate abundance and refuelling rates of shorebirds during stopover, which led to shorter stopover duration for juveniles and a higher probability of stopover outside of James Bay for all groups except white-rumped sandpiper. Finally, I estimated the relative importance of intertidal salt marsh and flat habitats to the diets of small shorebirds and found that semipalmated and white-rumped sandpiper (Calidris pusilla and C. fuscicollis) and semipalmated plover (Charadrius semipalmatus) diets consist of ~ 40 – 75% prey from intertidal marsh habitats, the highest documented in the Western Hemisphere for each species. My research shows that James Bay is of high importance to white-rumped sandpipers, which are unlikely to stop in North America after departing James Bay en route to southern South America. Additionally, intertidal salt marsh habitats (and Diptera larvae) appear particularly important for small shorebirds in the region. My thesis shows that changing environmental conditions, such as droughts, can affect shorebird refuelling and stopover strategies. Author Keywords: body condition, diet, environmental change, migration, ornithology, stopover ecology

Pages

Description

Graduate student theses produced at Trent University. You may also browse theses and dissertations by year, program, or author.

In collections

Search Our Digital Collections

Query

Enabled Filters

  • (-) ≠ Master of Arts
  • (-) = Environmental and Life Sciences
  • (-) ≠ Stotesbury

Filter Results

Date

2004 - 2024
(decades)
Specify date range: Show
Format: 2024/04/18

Collection

Author Name

Show more

Name (Any)

Show more

Degree

Subject (Topic)

Show more